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- PDB-1pta: THREE-DIMENSIONAL STRUCTURE OF PHOSPHOTRIESTERASE: AN ENZYME CAPA... -

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Basic information

Entry
Database: PDB / ID: 1pta
TitleTHREE-DIMENSIONAL STRUCTURE OF PHOSPHOTRIESTERASE: AN ENZYME CAPABLE OF DETOXIFYING ORGANOPHOSPHATE NERVE AGENTS
ComponentsPHOSPHOTRIESTERASEAryldialkylphosphatase
KeywordsHYDROLASE (ORGANOPHOSPHATE-DEGRADING)
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBenning, M. / Holden, H.M.
Citation
Journal: Biochemistry / Year: 1994
Title: Three-dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents.
Authors: Benning, M.M. / Kuo, J.M. / Raushel, F.M. / Holden, H.M.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure of the Binuclear Metal Center of Phosphotriesterase
Authors: Benning, M.M. / Kuo, J.M. / Raushel, F.M. / Holden, H.M.
History
DepositionJul 7, 1994Processing site: BNL
Revision 1.0Dec 1, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOTRIESTERASE


Theoretical massNumber of molelcules
Total (without water)35,4871
Polymers35,4871
Non-polymers00
Water2,324129
1
A: PHOSPHOTRIESTERASE

A: PHOSPHOTRIESTERASE


Theoretical massNumber of molelcules
Total (without water)70,9732
Polymers70,9732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3120 Å2
ΔGint-22 kcal/mol
Surface area25620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.200, 93.700, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PHOSPHOTRIESTERASE / Aryldialkylphosphatase


Mass: 35486.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brevundimonas diminuta (bacteria)
References: UniProt: P0A434, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein 1drop
210 mMHEPES1drop
39 %PEG80001reservoir
4100 mMbicine1reservoir
55 mM1reservoirNaN3
61 M1reservoirLiCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.09 Å / Lowest resolution: 100 Å / Num. obs: 21816 / % possible obs: 93 % / Num. measured all: 93927 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 2.09 Å / Lowest resolution: 2.2 Å / % possible obs: 88 % / Num. unique obs: 2551 / Num. measured obs: 8985 / Rmerge(I) obs: 0.171

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.1→30.1 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.18 20330 93 %
Refinement stepCycle: LAST / Resolution: 2.1→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 0 129 2568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.32
X-RAY DIFFRACTIONt_dihedral_angle_d17.1
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.012
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.1

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